Unknown,Transcriptomics,Genomics,Proteomics

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Alteration of the transcriptome upon plakophilin3 loss in FBM cell line

ABSTRACT: To understand alterations in gene expression upon plakophilin3 (PKP3) loss, we generated two FBM derived plakophilin3 knockdown clones. One of these clones named shpkp3-2 was used for the experiment. The gene expression profile of shpkp3-2 was compared with the vector control named vec. RNA used for this experiment was obtained from two biological replicates of vec (vec1 and vec2) and shpkp3-2 ( shpkp3-2-1 and shpkp3-2-2 ). RNA from the clones were obtained at separate time points in 2 groups. The first group was vec1 and shpkp3-2-1 and the second group was of clones vec2 and shpkp3-2-2 respectively.

ORGANISM(S): Homo sapiens

SUBMITTER: Srikanta Basu

PROVIDER: E-GEOD-61512 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Previously, we have identified the polypeptide N-acetylgalactosaminyltransferase 3 (GALNT3) gene as notably hypomethylated in low-malignant potential (LMP) and high-grade (HG) serous epithelial ovarian tumors, compared to normal ovarian tissues. Here we show that GALNT3 is strongly overexpressed in both LMP and HG serous EOC tumors, thus suggesting that epigenetic mechanisms might be implicated in GALNT3 overexpression in serous epithelial ovarian cancer (EOC). Moreover, GALNT3 expression significantly correlated with shorter progression-free survival (PFS) periods in serous EOC patients with advanced disease. Knockdown of the GALNT3 expression in EOC cells led to sharp decrease of cell proliferation and induced S-phase cell cycle arrest. Additionally, GALNT3 suppression significantly inhibited EOC cell migration and invasion. Gene expression profiling and consecutive network and pathway analyses confirmed these findings, as numerous genes and pathways known previously to be implicated in ovarian tumorigenesis, including EOC tumor invasion and metastasis, were found to be downregulated upon GALNT3 suppression, while some tumor suppressor genes were induced. Moreover, GALNT3 downregulation was associated with reduced MUC1 protein expression in EOC cells, probably related to destabilization of the MUC1 protein due to lack of GALNT3 glycosylation activity.Taken together, our data are indicative for a strong oncogenic potential of the GALNT3 gene in advanced EOC and identify this transferase as a novel EOC biomarker and putative EOC therapeutic target. Our findings also suggest that GALNT3 overexpression might contribute to ovarian etiology through aberrant mucin O-glycosylation. To better understand the molecular mechanisms of GALNT3 gene action in ovarian cancer cells, we employed the Agilent Whole Human Genome microarrays, containing ~ 44,000 genes to identify global gene expression changes upon GALNT3 suppression in A2780s cells. We compared the gene expression of the previously selected clone shRNA- GALNT3-knockdown clones 1 & 2 (sh-cl1 & sh-cl2) against the corresponding control (ctrl) clone. The microarray experiments were performed in duplicates, as four hybridizations were carried out for the GALNT3-suppressing cell clones against the corresponding control, using a fluorescent dye reversal (dye-swap) technique.

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Alteration of the transcriptome upon plakophilin3 loss in FBM cell line

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